[gmx-users] Need to confirm parameters.

[Justin Lemkul]

On 5/23/17 8:03 AM, Sailesh Bataju wrote:
>> The easiest thing to do
>> (solving this issue and #1) is to create an isobutane .rtp entry and have
>> pdb2gmx do all the work for you.  It's very simple to do.
>
>> -Justin
>
> Thank you sir, I've exactly followed your steps. I've created
> isobutane.rtp file and modified residuetypes.dat file by adding IBUT
> as Protein and then created PDB file from prodrg server. Then using
> pdb2gmx command finally got this result:
>
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
> Reading prodrg_ibut.pdb...
> WARNING: all CONECT records are ignored
> Read 14 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 1 residues with 14 atoms
>
>   chain  #res #atoms
>   1 ' '     1     14
>
>
> WARNING: there were 4 atoms with zero occupancy and 8 atoms with
>          occupancy unequal to one (out of 14 atoms). Check your pdb file.
>
> Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
> Atomtype 412
> Reading residue database... (charmm36)
> Opening force field file /usr/share/gromacs/top/charmm36.ff/isobutane.rtp
> Residue 1
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb
> Processing chain 1 (14 atoms, 1 residues)
> Identified residue IBUT0 as a starting terminus.
> Identified residue IBUT0 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> No suitable end (N or 5') terminus found in database - assuming this residue
> is already in a terminus-specific form and skipping terminus selection.
> No suitable end (C or 3') terminus found in database - assuming this residue
> is already in a terminus-specific form and skipping terminus selection.
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 1 residues with 14 atoms
> Making bonds...
> Warning: Short Bond (5-1 = 0.0259999 nm)
> Warning: Long Bond (5-6 = 0.99084 nm)
> Warning: Long Bond (1-2 = 0.944378 nm)
> Warning: Long Bond (1-3 = 0.895661 nm)
> Warning: Long Bond (1-4 = 0.866986 nm)
> Warning: Long Bond (7-8 = 0.502204 nm)
> Warning: Long Bond (7-9 = 0.567317 nm)
> Warning: Long Bond (7-10 = 0.92202 nm)
> Warning: Long Bond (11-12 = 0.592831 nm)
> Warning: Long Bond (11-13 = 0.700231 nm)
> Warning: Long Bond (11-14 = 0.729592 nm)
> Number of bonds was 13, now 13
> Generating angles, dihedrals and pairs...
> Before cleaning: 27 pairs
> Before cleaning: 27 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are   27 dihedrals,    0 impropers,   24 angles
>             27 pairs,       13 bonds and     0 virtual sites
> Total mass 58.124 a.m.u.
> Total charge 0.000 e
> Writing topology
>
> Writing coordinate file...
> 		--------- PLEASE NOTE ------------
> You have successfully generated a topology from: prodrg_ibut.pdb.
> The Charmm36 force field is used.
> 		--------- ETON ESAELP ------------
>
>
> 1. According to the first warning like this "there were 4 atoms with
> zero occupancy and 8 atoms with  occupancy unequal to one (out of 14
> atoms)"
>
> Is that a kind of error. Did I do any mistake as it said?
>

That's not an error and is irrelevant.

The short bond warnings do, however, indicate that the starting geometry is bad.

> 2. If i don't add IBUT as Protein in residuetypes.dat file I get error
> like this however I get same topol.top file.
>
> "Back Off! I just backed up topol.top to ./#topol.top.1#
> Processing chain 1 (14 atoms, 1 residues)
> Warning: Starting residue IBUT0 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program:     gmx pdb2gmx, version 2016.3
> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)
>
> Fatal error:
> Residue 'IBUT' not found in residue topology database"
>
> I've no idea whether I've successfully generated those files.
>

This fatal error has nothing to do with residuetypes.dat - it says that IBUT is 
not in the .rtp file.  But the above text says it completed successfully.  You 
don't need to denote IBUT as Protein, but there's no harm either way.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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